I think you are being unrealistically harsh on yourself. If I understand you correctly, you donate x% to a charity, and are now adding even more money by selling used manga. You wonder whether this is just an elaborate way of justifying your manga consumption.

I don't see why your manga consumption would require any justification! If physical manga are something you enjoy, it is completely fine to enjoy them. Selling them afterwards to donate more to charity seems like a good move that combines something you like and a way to go above and beyond in your donations. 

The question of why not more donations can always be asked, and this will lead to unrealistically high expectations, miserable lives and burnt-out EAs, all of which is not the most effective way to be. Hence, we set artificial points such as 10% of income (1% for students) as a point to no longer feel obliged to worry about donations. That you seem to have found a way to go above and beyond that point while allowing you to pursue a hobby is not weird or immoral, but rather laudable!

From a consequentialist perspective, I think you're better off sticking to digital — it takes a lot of time to sell things online, and you could be using that time for some combination of work and fun that would leave everyone better off (unless you place a very high value on physical manga).

Low-confidence idea: It might help to find some small ritual/mantra that you can use when you donate (or invest, etc.) the money you would have spent on physical manga — something along the lines of "I'm making the right decision" or "this is better for everyone".